The Disadvantages

The text will be stored and edited outside of Tinderbox (with perhaps a copy inside Tinderbox), not in Tinderbox's XML form. Therefore, within Tinderbox styles and links will not be visible, only the plain text markup that creates them. So you can use this technique, for example, on a rich text (.rtf) document, and have it open in TextEdit automatically, where you will see your styled text. But if you look at the note in Tinderbox, you see the rich text formatting markup.

More serious is the matter of links. You can still have "basic links" from and to notes, but you give up internal text links. (These are what you get when you select text in a note and make a link to another note.) You don't merely give up the styling of the link and the ability to follow it with a click, but the powerful ability to make a reference to another note within the Tinderbox document. You can still have arbitrary URLs ("web links") and generalizations of them used in other markup contexts, such as hyperref for latex; you will see the raw markup code within Tinderbox, of course.

There is a little annoyance: when you open the note you want to edit, it stays open within Tinderbox while you are editing it in your external editor. When you go back to Tinderbox you have to close it, and not just to reduce clutter: if you leave it open, then it will fail to be updated when you click in the Network window. Your notes and files will get out of sync. (This confused me when I first tried out the program and clicked the network update button while watching the note window that I expected to become filled with the contents of the URL, and nothing happened. It is claimed that this behavior is a feature.)

There is the possibility of getting confused and losing edits: if you open one of the files "directly" rather than from Tinderbox you might open a file generated by export by mistake rather than the "source" file. The next time you export you will destroy your changes. The appearance of generated markup in the file you are about to edit should be a clue, but to be safe put a comment in your template that adds a warning to the exported files: "This file is generated by Tinderbox: DO NOT EDIT". This sort of thing happens all over unix, where we have makefiles generated by configuration scripts, man pages made from source files, and you always need to make sure that you are editing an original rather than a generated document.